siwolf/score

SCORE - a consensus tool for detecting differentially expressed genes in bacteria

score's Issues

Build Docker Container

Conda not able to install packages labeled 'broken'

Thanks for the nice software!

When installing the dependencies through Snakemake + Conda, some YAML files refer to packages labeled 'broken'. To the best of my knowledge, these cannot be installed through Snakemake (however manually you can set e.g. -c bioconda/labels/broken to include them, but I haven't seen an option with Snakemake to do this).

AFAIK this only concerns score_deg_environment.yml. The error message is:

Creating conda environment libraries/env/score_deg_environment.yml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /project/vdputten/Kees/RM/SCORE-1.0.1/libraries/env/score_deg_environment.yml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound:
  - libgfortran-ng==7.5.0=hdf63c60_6
  - gxx_impl_linux-64==7.5.0=hdf63c60_6
  - gfortran_impl_linux-64==7.5.0=hdf63c60_6
  - gcc_impl_linux-64==7.5.0=hd420e75_6

Replacing the tags with tags from the same version but a different build might work

error running

Hi @SiWolf

I am trying to run this pipeline but unfortunately I get an error. Any idea how to solve it? I have already added my fasta and gff files to the reference folder and I have updated the metadata file. But i keep getting the same error.

`(score) sam@bioinf-pc:~/Downloads/SCORE$ bash run-SCORE.sh 2 PE
rm: cannot remove '.gz': No such file or directory
rm: cannot remove '.idx': No such file or directory
rm: cannot remove 'kallisto/sample*': No such file or directory
rm: cannot remove '.rda': No such file or directory
rm: cannot remove '.txt': No such file or directory
rm: cannot remove 'consensus*': No such file or directory
rm: cannot remove 'deg*': No such file or directory
rm: cannot remove 'diffexpr*': No such file or directory
rm: cannot remove 'filtered*': No such file or directory
rm: cannot remove 'genes*': No such file or directory
rm: cannot remove 'hmmer*': No such file or directory
rm: cannot remove 'pathway*': No such file or directory
rm: cannot remove 'proteins*': No such file or directory
rm: cannot remove 'transcript*': No such file or directory
rm: cannot remove 'summary*': No such file or directory
rm: cannot remove 'benchmarking*': No such file or directory
rm: cannot remove 'log.txt': No such file or directory
rm: cannot remove 'references/.tmp': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '.sam': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '': No such file or directory
FileNotFoundError in line 203 of /home/sam/Downloads/SCORE/SCORE_PE.snk:
[Errno 2] No such file or directory: 'references/027-annot.gff'
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 218, in
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 203, in verfify_id_combination
FileNotFoundError in line 203 of /home/sam/Downloads/SCORE/SCORE_PE.snk:
[Errno 2] No such file or directory: 'references/027-annot.gff'
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 218, in
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 203, in verfify_id_combination

real 0m0,157s
user 0m0,133s
sys 0m0,025s
`